A survey of CIN measures across mechanistic models

Abstract

Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, 6-centromere FISH, bulk transcriptomics, and single cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples correlated well (R=0.77; p<0.01) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also correlate well (R=0.77; p<0.01) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, single-cell DNA sequencing (scDNAseq) detects CIN with high sensitivity, and correlates very well with imaging methods (R=0.83; p<0.01). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division (MDD). This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.

KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells

“…Traditional methods for detecting aneuploidy, such as whole genome sequencing (WGS), rely on bulk averaging of cell populations, effectively masking heterogeneity among individual cells and preventing proper assessment of the extent or rate of chromosomal instability. Single-cell approaches, particularly single-cell DNA sequencing (scDNA-seq), overcome this limitation and can instead detect the full complement of distinct karyotypes present in a tumor [7][8][9][10][11] . These data can be used to reassemble the evolution of the tumor's cells, which can provide insights into how aneuploidy and chromosomal instability may drive tumorigenesis or inform treatments for therapeutic resistance 6,9 .…”